ATAC-Seq/ RNA-Seq (PND15 vs Adults): TF motifs overlap and diff exp genes

Library

library(plotly)

Data

load("./input/limma_SC_Controls.RData")
dea <- dea.limma$`PND15 vs Adult`
colnames(dea) <- paste("DEA", colnames(dea), sep = "_")

dea <- dea[abs(dea$DEA_logFC) >= 1 & dea$DEA_adj.P.Val <= 0.05,]

tf <- readxl::read_xlsx(path = "input/atac_diff_acc_tfbs_hocomoco_overlap.xlsx", sheet = 1, trim_ws = T)

Map with Genes

tab <- merge(tf, dea, by.y = "DEA_Genes", by.x = "TF-Transcription factor")

Save table

writexl::write_xlsx(tab, "./output/dea_genes_overlap_tf_motifs.xlsx", col_names = T, format_headers = T)

Plot for TF overlapping DEGs

plot_ly(
  data = tab, x = tab$DEA_logFC, y = tab$`diffAccessibility-logFC`,
  marker = list(size = 5, color = "blue"),
  text = ~ paste(
    "Gene: ", tab$`Peak-SYMBOL`,
    "<br>Name: ", tab$`Peak-GENENAME`,
    "<br>Annotation: ", tab$`Peak-annotation`,
    "<br>DA logFC: ", tab$`diffAccessibility-logFC`,
    "<br>DA FDR: ", tab$`diffAccessibility-qvalue`,
    "<br>DE logFC: ", tab$DEA_logFC,
    "<br>DE FDR: ", tab$DEA_adj.P.Val
  ),
  hoverinfo = "text"
) %>%
  layout(
    title = "TF Motifs overlapping differentially expressed genes",
    yaxis = list(title = "logFC: Differential Accessibility (DA)"),
    xaxis = list(title = "logFC: Differential Expression (DE)")
  )

SessionInfo

devtools::session_info()
## ─ Session info ───────────────────────────────────────────────────────────────
##  setting  value                       
##  version  R version 3.6.2 (2019-12-12)
##  os       Ubuntu 16.04.6 LTS          
##  system   x86_64, linux-gnu           
##  ui       X11                         
##  language (EN)                        
##  collate  en_US.UTF-8                 
##  ctype    en_US.UTF-8                 
##  tz       Europe/Zurich               
##  date     2020-01-16                  
## 
## ─ Packages ───────────────────────────────────────────────────────────────────
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## [2] /usr/local/lib/R/site-library
## [3] /usr/lib/R/site-library
## [4] /usr/lib/R/library
## [5] /home/ubuntu/softwares/anaconda3/pkgs

Deepak Tanwar

Created on: 2019-11-29
Updated on: 2020-01-16